Fuzzier Logic
In a rare move, I’m going to largely copy across a post from my work blog, because I hope it contains useful information. For background, I’m trying to write a simple python script that extracts particular metadata from a .RAW file, produced by a Thermo Finnigan mass spectrometer. Tools that exist for parsing these files require access to proprietary XCalibur libraries, which I do not have.
Thermo provided a link to MSFileReader, a ‘freeware’ COM object that should allow interaction with RAW files without an XCalibur installation. They also sent a PDF guide to the COM object. Although this will allow XCalibur to be avoided, the work is still Windows-bound.
Python and COM objects
Python can talk to COM objects, through the win32com.client package. As a test, I installed Python and MSFileReader and the pywin32 libs on my netbook (which is a Windows 7 machine). Can import the required Python module, but need to extent the PATH somewhat:
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>>> sys.path.append('C:\\Python26\\Lib\\site-packages\\win32')
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>>> sys.path.append('C:\\Python26\\Lib\\site-packages\\win32\\lib')
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>>> from win32com.client import Dispatch
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>>> x = Dispatch("NAME")
The key thing here is “NAME”:
The provided PDF gives C snippets for each method available in the COM object. This only provides one clue as to the possible name of the COM object
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// example for Open
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TCHAR* szPathName[] = _T(“c:\\xcalibur\\examples\\data\\steroids15.raw”);
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long nRet = XRawfileCtrl.Open( szPathName );
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if( nRet != 0 ) {
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::MessageBox( NULL, _T(“Error opening file”), _T(“Error”), MB_OK );
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…
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}
XRawfileCtrl is used to call the Open() method. However, this and MSFileReader as “NAME” both fail (Invalid class string).
Found ‘multiplierz‘ which seems to use MSFileReader to create mzAPI – which focusses on access to the actual data, rather than the metadata. The code gives some good clues as to how to use the COM object. [doi:10.1186/1471-2105-10-364]
MSFileReader.XRawfile is used as “NAME” in this code.
So:
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>>> sys.path.append('C:\\Python26\\Lib\\site-packages\\win32')
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>>> sys.path.append('C:\\Python26\\Lib\\site-packages\\win32\\lib')
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>>> from win32com.client import Dispatch
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>>> x = Dispatch("MSFileReader.XRawfile")
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>>> x.Open("C:\\Users\\path\\to\\file\\msfile.RAW")
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>>>
To be continued…
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Hi,
I’m trying too to parse the Thermo .raw files, did you continue this quest any further ? I would be very glad to hear from this ! Thanks and keep going